grinch | global report investigating novel coronavirus haplotypes

B.1.1.7 report 2021-01-07



Data source and processing

This report is recent as of 2021-01-06 12:08 GMT. All SARS-CoV-2 sequences were downloaded from GISAID and genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.

The sequences were then assigned lineages with pangolin v2.1.6, pangoLEARN version 2020-12-17-2.

Pangolin assigns B.1.1.7 to sequences with more than 4 of the 17 defining B.1.1.7 SNPs – defined here

Table 1 | Summary of sequence data

Lineage Country count Country Sequence count Earliest sequence Travel history
B.1.1.7 28 UK 7711, Denmark 76, Portugal 35, Italy 24, Finland 14, France 14, Netherlands 13, Australia 10, Sweden 9, USA 9, Singapore 7, Ireland 7, Switzerland 6, New_Zealand 6, Germany 5, Spain 4, Jamaica 4, Israel 4, South_Korea 3, India 3, Luxembourg 3, Hong_Kong 3, Norway 2, Brazil 2, Pakistan 2, Canada 1, Oman 1, Lebanon 1 7979 2020-09-20

Lineage B.1.1.7

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Table B.1.1.7 | Lineage B.1.1.7

Statistic Information
Sequence count 7979
Countries with sequences 28
Countries reported 45
Likely origin United Kingdom
SNPs aa:orf1ab:T1001I
aa:orf1ab:A1708D
aa:orf1ab:I2230T
del:11288:9
del:21765:6
del:21991:3
aa:S:N501Y
aa:S:A570D
aa:S:P681H
aa:S:T716I
aa:S:S982A
aa:S:D1118H
aa:Orf8:Q27*
aa:Orf8:R52I
aa:Orf8:Y73C
aa:N:D3L
aa:N:S235F

Figure 1 | Cumulative sequence count over time B.1.1.7

2021-01-07T16:42:50.643597 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/ 2020-09-15 2020-10-01 2020-10-15 2020-11-01 2020-11-15 2020-12-01 2020-12-15 2021-01-01 Date 0 500 1000 1500 2000 2500 3000 Sequence count 0 2000 4000 6000 8000 Total

Figure 2 | Date of earliest B.1.1.7 detected

2021-01-07T16:42:48.735400 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/ 2020-09-20 2020-11-29 2020-12-07 2020-12-13 2020-12-15 2020-12-18 2020-12-20 2020-12-22 2020-12-25

Figure 3 | Map of B.1.1.7 sequence counts

2021-01-07T16:42:49.036709 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/ Max sequences 1 sequence No variant record

Figure 4 | Sequence count per country B.1.1.7

2021-01-07T16:42:49.773357 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/ United Kingdom Denmark Portugal Italy Finland France Netherlands Australia Sweden United States Of America Singapore Ireland Switzerland New Zealand Germany Spain Jamaica Israel South Korea India Luxembourg Hong Kong Norway Brazil Pakistan Canada Oman Lebanon Country 1 10 100 1000 10000 Sequence count (log10) 7711 76 35 24 14 14 13 10 9 9 7 7 6 6 5 4 4 4 3 3 3 3 2 2 2 1 1 1

Figure 5 | Frequency B.1.1.7 in sequences produced since first new variant reported per country

2021-01-07T16:42:51.062258 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/ Spain Norway Brazil Pakistan Ireland Lebanon Finland Jamaica South Korea France Oman Italy India Israel New Zealand Canada Hong Kong Sweden Singapore United Kingdom Portugal Australia Luxembourg Netherlands Germany United States Of America Switzerland Denmark Country 0.0 0.2 0.4 0.6 0.8 1.0 Frequency 4/4 2/2 2/2 2/2 7/7 1/1 14/15 4/5 3/4 14/20 1/2 24/53 3/9 4/12 6/19 1/4 3/13 9/49 7/61 7711/84641 35/429 10/181 3/91 13/436 5/175 9/474 6/418 76/11379

Figure 6 | B.1.1.7 count per country

2021-01-07T16:42:51.606745 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/ 2020-10-01 2020-10-15 2020-11-01 2020-11-15 2020-12-01 2020-12-15 2021-01-01 Date 1 3 10 31 100 316 Count (7 day rolling average) United Kingdom Italy Portugal Finland Netherlands Denmark

Figure 7 | Rolling average B.1.1.7 frequency per country

2021-01-07T16:42:51.367849 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/ 2020-10-01 2020-10-15 2020-11-01 2020-11-15 2020-12-01 2020-12-15 2021-01-01 Date 0.0 0.2 0.4 0.6 0.8 Frequency (7 day rolling average) United Kingdom Italy Portugal Finland Netherlands Denmark

Figure 8 | Map of B.1.1.7 local transmission

2021-01-07T16:42:49.303897 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/ status_unknown imported_only local_transmission No variant recorded

Figure 6 | Air traffic from UK by destination

The number of ticketed origin-to-destination journeys from London airports to countries outside the United Kingdom during October 2020.

Colours indicate numbers of published genomes of B.1.1.7 deposited on GISAID. Grey bars indicate countries that have reported the presence of the variant but have not yet published B.1.1.7 sequences on GISAID. White bars indicate countries with no reports of B.1.1.7.

Flight data come from the International Air Transportation Association that capture anonymized, passenger-level flight itinerary data, comprising both commercial flights and scheduled charter flights. These data account for ~90% of global air travel volumes, with the remaining volumes modelled using market intelligence. We report data from destinations including >5,000 passengers.

Note that flight data reflects final-destination on a booked journey, we cannot account for instances where two separate tickets were purchased.

Data from Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer

2021-01-07T16:42:48.350011 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/ 0 20000 40000 60000 80000 100000 120000 Total Number of Passengers Spain Italy Greece Poland Germany Portugal Turkey Romania Cyprus Ireland Bulgaria France Sweden India United States of America Lithuania United Arab Emirates Netherlands Pakistan Denmark Hungary Switzerland Egypt Nigeria China Russia Slovakia Albania Moldova Malta Ukraine Israel Austria Latvia Czech Republic Jamaica Norway Morocco Country 0 1 2 3 4 5 6 7 9 10 13 14 24 35 76 Reported

Table 2 | Reported B.1.1.7 imports.

Country count: 45

Country Earliest report Date local transmission Local transmission Method of surveillance Source
United States of America 27/12/2020 27/12/2020 1 SGTF https://eu.usatoday.com/story/news/health/2020/12/29/colorado-reports-first-known-us-case-new-covid-strain-uk/4079697001/ | https://twitter.com/K_G_Andersen/status/1344825028370567169/photo/1
Denmark 14/11/2020 1 community_sequencing https://www.bbc.co.uk/news/world-55382212
Australia 20/12/2020 0 travellers https://www.dw.com/en/covid-19-more-countries-detect-mutated-uk-coronavirus-variant/a-56009203
United Kingdom 20/09/2020 20/09/2020 1 community_sequencing https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563
Turkey 01/01/2021 0 travellers https://www.cnnturk.com/video/turkiye/son-dakika-haberi-bakan-koca-acikladi-15-kiside-mutasyonlu-virus-ingiltereden-girisler-tamamen-durduruldu-video
Belgium 20/12/2020 0 https://www.brusselstimes.com/news/belgium-all-news/146288/netherlands-bans-flights-from-uk-over-new-covid-mutation-found-coronavirus-van-ranst-who/
Canada 26/12/2020 26/12/2020 1 https://www.cbc.ca/news/canada/toronto/ontario-confirms-first-cases-covid19-uk-variant-1.5855361
Chile 22/12/2020 0 travellers https://www.reuters.com/article/uk-health-coronavirus-britain-variants-f/chile-records-first-case-of-british-variant-of-coronavirus-health-ministry-idUSKBN2931CS
China 04/12/2020 0 travellers http://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2020.270 | https://www.globaltimes.cn/page/202101/1211644.shtml
Finland 28/12/2929 0 travellers https://yle.fi/uutiset/osasto/news/new_uk_variant_covid_strain_detected_in_finland/11716211
France 19/12/2020 06/01/2021 1 https://www.aljazeera.com/news/2020/12/26/france-confirms-first-case-of-new-coronavirus-variant | https://cnnphilippines.com/news/2021/1/6/Hong-Kong-detects-UK-COVID-19-variant-from-Manila-outbound-passenger-.html
Germany 27/11/2020 27/11/2020 1 travellers https://www.ms.niedersachsen.de/startseite/service_kontakt/presseinformationen/variante-des-corona-virus-aus-grossbritannien-erstmals-in-niedersachsen-nachgewiesen-195841.html
Iceland 21/12/2020 0 travellers https://icelandmonitor.mbl.is/news/news/2020/12/30/eleven_recent_cases_of_british_variant_of_coronavir/
India 18/12/2020 0 travellers https://www.republicworld.com/india-news/general-news/maharashtra-8-patients-detected-with-uk-variant-of-covid-19-5-from-mumbai.html
Ireland 25/12/2020 29/12/2020 1 travellers https://www.independent.ie/world-news/coronavirus/new-uk-variant-of-covid-19-confirmed-in-ireland-while-1025-new-cases-and-two-further-deaths-confirmed-39900087.html | https://www.thejournal.ie/uk-strain-coronavirus-b117-ireland-third-wave-5314440-Jan2021/
Israel 23/12/2020 01/01/2020 1 https://www.timesofisrael.com/health-officials-fear-mutant-strain-spreading-as-they-examine-dozens-of-tests/ | https://menafn.com/1101373506/Mutant-COVID-19-variant-affects-18-more-people-in-Israel&source=30
Italy 20/12/2020 23/12/2020 1 https://news.sky.com/story/covid-19-new-strain-found-in-denmark-netherlands-and-australia-says-who-12169262 | https://www.aa.com.tr/en/europe/italy-detects-new-case-of-coronavirus-variant/2086553
Japan 25/12/2020 0 travellers https://www.theguardian.com/world/2020/dec/25/japan-reports-cases-coronavirus-variant-spreading-across-uk
Jordan 27/12/2020 0 travellers https://medicalxpress.com/news/2020-12-jordan-coronavirus-variant-cases-minister.html
Lebanon 21/12/2020 0 travellers https://www.aljazeera.com/news/2020/12/26/france-confirms-first-case-of-new-coronavirus-variant
Malta 19/12/2020 0 travellers https://timesofmalta.com/articles/view/uk-covid-19-variant-detected-in-malta.841925
Netherlands 20/12/2020 28/12/2020 1 https://www.bbc.co.uk/news/world-55382212 | https://www.rivm.nl/en/news/spread-of-uk-coronavirus-variant-in-netherlands
Norway 27/12/2020 0 travellers https://news.sky.com/story/covid-19-france-discovers-its-first-case-of-the-new-coronavirus-variant-after-frenchman-travelled-from-london-12172620
Pakistan 29/12/2020 0 travellers https://www.hindustantimes.com/world-news/first-confirmed-case-of-new-covid-19-strain-detected-in-pakistan/story-TFLSMYU6WRJ8yToNQfIeyJ.html
Portugal 27/12/2020 28/12/2020 1 travellers https://www.sapo.pt/noticias/atualidade/covid-19-nova-estirpe-e-recente-em-portugal-e_5ff221926def8e5d02b29e94;https://www.portugalresident.com/madeira-registers-first-18-cases-of-new-covid-variant-one-from-lisbon-area/
Singapore 23/12/2020 0 travellers https://www.straitstimes.com/singapore/singapore-confirms-1-imported-patient-with-potentially-more-contagious-covid-19-strain
South Korea 22/12/2020 0 travellers https://www.dailymail.co.uk/news/article-9091763/S-Korea-accelerate-virus-vaccine-efforts-U-K-variant-detected.html
Spain 26/12/2020 https://www.theguardian.com/world/2020/dec/26/spain-and-sweden-report-cases-of-uk-covid-variant
Sweden 20/12/2020 0 https://www.svt.se/nyheter/lokalt/sormland/fall-av-den-brittiska-virusvarianten-upptack-i-sormland
Taiwan 30/12/2020 0 travellers https://www.scmp.com/news/china/science/article/3115884/taiwan-reports-its-first-case-mutant-covid-19-strain-found
United Arab Emirates 29/12/2020 0 travellers https://www.khaleejtimes.com/coronavirus-pandemic/new-covid-strain-in-uae-all-we-know-so-far
Switzerland 24/12/2020 05/01/2021 1 https://www.bag.admin.ch/bag/fr/home/das-bag/aktuell/medienmitteilungen.msg-id-81829.html | https://www.swissinfo.ch/eng/more-variant-covid-19-carriers-detected-in-switzerland/46262070
Brazil 21/12/2020 0 SGTF https://www.dropbox.com/s/y99g4uw6s7za01c/CADDE%20genomic%20report%2031%20Dec%202020.pdf?dl=0
Vietnam 24/12/2020 0 travellers https://www.telegraph.co.uk/news/2021/01/02/vietnam-reports-first-case-new-coronavirus-variant-woman-returning/
Luxembourg 29/12/2020 0 travellers https://covid19.public.lu/fr/actualite-covid-19/communiques/2021/01/02-covid-variante.html
New Zealand 25/12/2020 0 travellers https://www.rnz.co.nz/news/national/433973/covid-19-update-19-new-imported-cases-in-past-three-days
Hong Kong 23/12/2020 0 travellers https://uk.reuters.com/article/us-health-coronavirus-hongkong/uk-coronavirus-variant-likely-found-in-hong-kong-as-city-secures-vaccine-supplies-idUKKBN28X1E1
Cyprus 20/12/2020 0 travellers https://cyprus-mail.com/2021/01/03/coronavirus-new-fast-spreading-british-strain-found-in-cyprus/
Thailand 03/01/2020 0 travellers https://www.thestar.com.my/aseanplus/aseanplus-news/2021/01/03/thailand-finds-new-strain-of-covid-19-from-uk-in-four-britons
Greece 03/01/2020 0 travellers https://www.keeptalkinggreece.com/2021/01/03/covid19-mutated-strain-greece-travelers-uk/#.X_IT0OugNCg.twitter
Jamaica 21/12/2020 0 travellers https://www.thestkittsnevisobserver.com/new-corona-strain-arrives-in-jamaica-on-last-uk-flight/
Austria 04/01/2021 0 https://www.sn.at/panorama/wissen/live-corona-mutationen-sind-in-oesterreich-angekommen-97891537
Iran 05/01/2021 0 travellers https://www.jpost.com/breaking-news/iran-finds-first-case-of-new-virus-variant-in-traveler-from-uk-654329
Philippines 22/12/2020 1 https://cnnphilippines.com/news/2021/1/6/Hong-Kong-detects-UK-COVID-19-variant-from-Manila-outbound-passenger-.html
Oman 05/01/2021 0 travellers https://www.reuters.com/article/us-health-coronavirus-oman-idUSKBN29A1G9